MolNFT v1 · #117644 · protein
Crystal structure of carminomycin-4-O-methyltransferase dnrk in complex with sah and 2-chloro-4-nitrophenol
5EEH · Carminomycin 4-O-methyltransferase dnrk: “Crystal structure of carminomycin-4-O-methyltransferase dnrk in complex with sah and 2-chloro-4-nitrophenol”. X-ray diffraction, 3 ligands (P9P, SAH, SO4), 11 pockets (best druggability…
- PDB
- 5EEH
- Type
- protein
- Length
- 1,025 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carminomycin 4-O-methyltransferase dnrk
- EC
- 2.1.1.292
- UniProt
- Q06528
- Ligands
- P9P, SAH, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carminomycin 4-O-methyltransferase dnrk (EC 2.1.1.292) | protein | 342 | 50% helix, 17% strand | Q06528 |
| B | Carminomycin 4-O-methyltransferase dnrk (EC 2.1.1.292) | protein | 340 | 50% helix, 16% strand | Q06528 |
| C | Carminomycin 4-O-methyltransferase dnrk (EC 2.1.1.292) | protein | 343 | 48% helix, 17% strand | Q06528 |
Ligands and binding sites
- P9P · 2-chloranyl-4-nitro-phenol · ligand · 15 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.83 | 0.88 | 62 | SAH, P9P, SO4 |
| 2 | 547 | 0.82 | 0.87 | 56 | SAH, P9P, SO4 |
| 3 | 738 | 0.80 | 0.83 | 66 | SAH, P9P |
| 4 | 137 | 0.50 | 0.79 | 24 | empty |
| 5 | 81 | 0.41 | 0.79 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 795 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5EEH · Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06528 · AlphaFold monomer V2.0 prediction for carminomycin 4-O-methyltransferase dnrk (Q06528) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q06528
- Elsewhere: RCSB PDB 5EEH · PDBe 5EEH · UniProt Q06528
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